Negative Frequency‐Dependent Selection Promotes Strain Structure in a Plant Pathogen

Specific recognition of microbial virulence factors (effectors) by host defence proteins can generate negative frequency-dependent selection (NFDS), enabling the maintenance of strain diversity. Our characterisation of 76 Midwestern US Pseudomonas syringae strains and 1104 global strains confirmed high strain diversity, but also revealed that strains are structured into similarity modules, consistent with core genome phylogeny but unexplained by host, location or genetic linkage. We developed a stochastic computational model that embraces the large variability now known to characterise effector repertoires. We show that NFDS can not only generate modular strain structure but is required to maintain modularity under genetic exchange, for which there is evidence in the data. These modules form through the emergence of groups of pathogens virulent to dominant hosts at a given time. Thus, eco-evolutionary dynamics contribute to strain coexistence through flux in the modules that represent niches within the host population.